{pangoRo}

Peace of mind with PANGO Lineages

Allen O’Brien

Principal Data Scientist @ PHSA DARE

2023-08-30

Applied Epi Community

PANGO Lineages

  • Track spread of COVID-19 transmission
  • Document & classify lineages
  • Cluster of sequences associated with epidemiological event ref

Aliases

Short Name
BA.1

EG.1

Long Name
B.1.1.529.1

XBB.1.9.2.1

[BJ.1, BM.1.1.1]

BJ.1 → B.1.1.529.2.10.1.1
BM.1.1.1 → B.1.1.529.2.75.3.1.1.1

Alias struggles

  • String format, requires parsing
  • Hierarchical relationship
  • Countless strains

Install & Load {pangoRo}

Based upon the Python package pango_aliasor.

Install the package from GitHub…

remotes::install_github('al-obrien/pangoRo')


Load into session…

library(pangoRo)

Accessing reference tables

fetch_pango_summary_tbl()
alias lineage recomb
A FALSE
B FALSE
C B.1.1.1 FALSE
D B.1.1.25 FALSE
G B.1.258.2 FALSE
K B.1.1.277 FALSE
L B.1.1.10 FALSE
M B.1.1.294 FALSE
N B.1.1.33 FALSE
P B.1.1.28 FALSE
Q B.1.1.7 FALSE
R B.1.1.316 FALSE
S B.1.1.217 FALSE
U B.1.177.60 FALSE
V B.1.177.54 FALSE
W B.1.177.53 FALSE
Y B.1.177.52 FALSE
Z B.1.177.50 FALSE
AA B.1.177.15 FALSE
AB B.1.160.16 FALSE
AC B.1.1.405 FALSE
AD B.1.1.315 FALSE
AE B.1.1.306 FALSE
AF B.1.1.305 FALSE
AG B.1.1.297 FALSE
AH B.1.1.241 FALSE
AJ B.1.1.240 FALSE
AK B.1.1.232 FALSE
AL B.1.1.231 FALSE
AM B.1.1.216 FALSE
AN B.1.1.200 FALSE
AP B.1.1.70 FALSE
AQ B.1.1.39 FALSE
AS B.1.1.317 FALSE
AT B.1.1.370 FALSE
AU B.1.466.2 FALSE
AV B.1.1.482 FALSE
AW B.1.1.464 FALSE
AY B.1.617.2 FALSE
AZ B.1.1.318 FALSE
BA B.1.1.529 FALSE
BB B.1.621.1 FALSE
BC B.1.1.529.1.1.1 FALSE
BD B.1.1.529.1.17.2 FALSE
BE B.1.1.529.5.3.1 FALSE
BF B.1.1.529.5.2.1 FALSE
BG B.1.1.529.2.12.1 FALSE
BH B.1.1.529.2.38.3 FALSE
BJ B.1.1.529.2.10.1 FALSE
BK B.1.1.529.5.1.10 FALSE
BL B.1.1.529.2.75.1 FALSE
BM B.1.1.529.2.75.3 FALSE
BN B.1.1.529.2.75.5 FALSE
BP B.1.1.529.2.3.16 FALSE
BQ B.1.1.529.5.3.1.1.1.1 FALSE
BR B.1.1.529.2.75.4 FALSE
BS B.1.1.529.2.3.2 FALSE
BT B.1.1.529.5.1.21 FALSE
BU B.1.1.529.5.2.16 FALSE
BV B.1.1.529.5.2.20 FALSE
BW B.1.1.529.5.6.2 FALSE
BY B.1.1.529.2.75.6 FALSE
BZ B.1.1.529.5.2.3 FALSE
CA B.1.1.529.2.75.2 FALSE
CB B.1.1.529.2.75.9 FALSE
CC B.1.1.529.5.3.1.1.1.2 FALSE
CD B.1.1.529.5.2.31 FALSE
CE B.1.1.529.5.2.33 FALSE
CF B.1.1.529.5.2.27 FALSE
CG B.1.1.529.5.2.26 FALSE
CH B.1.1.529.2.75.3.4.1.1 FALSE
CJ B.1.1.529.2.75.3.1.1.1 FALSE
CK B.1.1.529.5.2.24 FALSE
CL B.1.1.529.5.1.29 FALSE
CM B.1.1.529.2.3.20 FALSE
CN B.1.1.529.5.2.21 FALSE
CP B.1.1.529.5.2.6 FALSE
CQ B.1.1.529.5.3.1.4.1.1 FALSE
CR B.1.1.529.5.2.18 FALSE
CS B.1.1.529.4.1.10 FALSE
CT B.1.1.529.5.2.36 FALSE
CU B.1.1.529.5.1.26 FALSE
CV B.1.1.529.2.75.3.1.1.3 FALSE
CW B.1.1.529.5.3.1.1.1.1.1.1.14 FALSE
CY B.1.1.529.5.2.7 FALSE
CZ B.1.1.529.5.3.1.1.1.1.1.1.1 FALSE
DA B.1.1.529.5.2.38 FALSE
DB B.1.1.529.5.2.25 FALSE
DC B.1.1.529.4.6.5 FALSE
DD B.1.1.529.2.3.21 FALSE
DE B.1.1.529.5.1.23 FALSE
DF B.1.1.529.5.10.1 FALSE
DG B.1.1.529.5.2.24.2.1.1 FALSE
DH B.1.1.529.5.1.22 FALSE
DJ B.1.1.529.5.1.25 FALSE
DK B.1.1.529.5.3.1.1.1.1.1.1.7 FALSE
DL B.1.1.529.5.1.15 FALSE
DM B.1.1.529.5.3.1.1.1.1.1.1.15 FALSE
DN B.1.1.529.5.3.1.1.1.1.1.1.5 FALSE
DP B.1.1.529.5.3.1.1.1.1.1.1.8 FALSE
fetch_pango_summary_tbl()
Lineage Most common countries Earliest date # designated # assigned Description WHO Name full_name
A.5 Spain 62.0%, United Kingdom 14.0%, Uruguay 5.0%, Portugal 2.0%, Peru 2.0% 2020-03-01 439 525 A lineage with a lot of representation from Spanish-speaking countries. A Spanish/ South-American lineage, but now with sequences from an outbreak in Scotland. Also now includes what was previously A.10. NA NA
B United States of America 40.0%, United Kingdom 15.0%, China 7.0%, Mexico 5.0%, Germany 3.0% 2019-12-24 4001 10237 One of the two original haplotypes of the pandemic(and first to be discovered) NA NA
B.1 United States of America 46.0%, Turkey 11.0%, United Kingdom 6.0%, Canada 4.0%, France 3.0% 2020-01-01 46228 118909 A large European lineage the origin of which roughly corresponds to the Northern Italian outbreak early in 2020. NA NA
B.1.1 United Kingdom 26.0%, United States of America 16.0%, Japan 6.0%, Russia 6.0%, Turkey 5.0% 2020-02-03 22790 51415 European lineage with 3 clear SNPs `28881GA`,`28882GA`,`28883GC` NA NA
B.1.1.7 United Kingdom 23.0%, United States of America 20.0%, Germany 9.0%, Sweden 6.0%, Denmark 6.0% 2020-02-07 69636 1115159 UK lineage of concern, associated with the N501Y mutation. More information can be found at cov-lineages.org/global_report.html NA NA
B.1.1.28 Brazil 79.0%, Philippines 9.0%, United States of America 4.0%, Paraguay 2.0%, Japan 1.0% 2020-02-10 854 5071 Brazil mostly, absorbed B.1.1.94 and B.1.1.143 NA NA
P.1 Brazil 58.0%, United States of America 26.0%, Chile 3.0%, Argentina 1.0%, Spain 1.0% 2020-04-07 29946 72579 Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutations with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. From #77 NA B.1.1.28.1
B.1.1.50 Israel 88.0%, Palestine 5.0%, United Kingdom 4.0%, Denmark 1.0%, United States of America 0.0% 2020-03-29 461 1464 Israel and Palestine NA NA
B.1.1.529 United States of America 35.0%, Germany 13.0%, India 9.0%, Turkey 5.0%, Russia 5.0% 2020-04-14 0 8043 South Africa and Botswana lineage, from pango-designation issue #343 NA NA
BA.1 United Kingdom 41.0%, United States of America 22.0%, Denmark 5.0%, Germany 4.0%, Brazil 4.0% 2020-06-25 66001 423104 Alias of B.1.1.529.1, from pango-designation issue #361 NA B.1.1.529.1
BA.1.1 United States of America 47.0%, United Kingdom 19.0%, Germany 7.0%, Canada 4.0%, France 2.0% 2020-01-27 104527 965459 Alias of B.1.1.529.1.1, from pango-designation issue #360 NA B.1.1.529.1.1
BA.1.1.14 United Kingdom 51.0%, United States of America 16.0%, Germany 6.0%, Spain 6.0%, Brazil 4.0% 2020-12-10 6372 19706 Alias of B.1.1.529.1.1.14, European lineage NA B.1.1.529.1.1.14
BA.1.15 United States of America 69.0%, United Kingdom 13.0%, Canada 3.0%, Germany 2.0%, Brazil 2.0% 2020-06-14 35340 181922 Alias of B.1.1.529.1.15, lineage in USA and other countries NA B.1.1.529.1.15
BA.1.17 Australia 27.0%, Spain 16.0%, United Kingdom 13.0%, United States of America 8.0%, Germany 6.0% 2020-11-06 11367 72251 Alias of B.1.1.529.1.17, European lineage NA B.1.1.529.1.17
BA.1.17.2 United Kingdom 67.0%, United States of America 6.0%, Canada 4.0%, Germany 4.0%, Denmark 3.0% 2020-10-23 29853 192714 Alias of B.1.1.529.1.17.2, lineage from pango-designation issue #462 NA B.1.1.529.1.17.2
BA.1.21 Norway 47.0%, Germany 9.0%, Italy 5.0%, South_Africa 5.0%, Denmark 5.0% 2021-01-09 4525 6914 Alias of B.1.1.529.1.21, lineage from pango-designation issue #505 NA B.1.1.529.1.21
BA.2 United Kingdom 29.0%, Germany 13.0%, Denmark 11.0%, United States of America 11.0%, France 7.0% 2020-03-28 111257 1187286 Alias of B.1.1.529.2, from pango-designation issue #361 NA B.1.1.529.2
BA.2.3 United States of America 25.0%, United Kingdom 17.0%, Canada 9.0%, Japan 8.0%, South_Korea 6.0% 2020-09-24 19173 108564 Alias of B.1.1.529.2.3, lineage in Philippines and other countries NA B.1.1.529.2.3
BA.2.3.2 Vietnam 29.0%, Japan 26.0%, United States of America 11.0%, Australia 6.0%, Laos 4.0% 2022-01-22 618 2239 Alias of B.1.1.529.2.3.2, Vietnam and Japan lineage NA B.1.1.529.2.3.2
BS.1.1 Japan 45.0%, Australia 16.0%, Vietnam 11.0%, South_Korea 7.0%, Denmark 4.0% 2022-08-20 13 461 Alias of B.1.1.529.2.3.2.1.1, Vietnam lineage, defined by S:K356T, from pango-designation issue #1097 NA B.1.1.529.2.3.2.1.1
CM.2.1 Australia 47.0%, Indonesia 27.0%, Singapore 5.0%, South_Korea 5.0%, Germany 5.0% 2022-10-30 7 60 Alias of B.1.1.529.2.3.20.2.1, Indonesia/Australia, S:F486S, issue #1356 NA B.1.1.529.2.3.20.2.1
CM.4.1 Japan 63.0%, Philippines 20.0%, United States of America 12.0%, Canada 1.0%, New_Zealand 1.0% 2022-09-25 36 203 Alias of B.1.1.529.2.3.20.4.1, S:K478R, Philippines/Japan/USA NA B.1.1.529.2.3.20.4.1
CM.7.1.1 France 42.0%, Spain 25.0%, Italy 25.0%, Israel 8.0% 2023-03-22 15 12 Alias of B.1.1.529.2.3.20.7.1, S:R403K, Europe, from sars-cov-2-variants/lineage-proposals#37 NA B.1.1.529.2.3.20.7.1
CM.8.1 United States of America 40.0%, Philippines 15.0%, Canada 14.0%, Japan 8.0%, South_Korea 6.0% 2022-10-16 248 1110 Alias of B.1.1.529.2.3.20.8.1, Australia/England, S:F486S NA B.1.1.529.2.3.20.8.1
CM.8.1.1 Singapore 86.0%, South_Korea 4.0%, Japan 3.0%, Malaysia 3.0%, Germany 1.0% 2022-12-12 24 90 Alias of B.1.1.529.2.3.20.8.1.1, Singapore/Malaysia, S:K147N NA B.1.1.529.2.3.20.8.1.1
FV.1 Japan 42.0%, South_Korea 22.0%, Philippines 10.0%, United States of America 6.0%, Dominican_Republic 4.0% 2023-01-29 11 200 Alias of B.1.1.529.2.3.20.8.1.1.1, S:R346T, M:E11Q, Singapore/SouthKorea/Japan/Philippines/HK NA B.1.1.529.2.3.20.8.1.1.1
CM.8.1.2 United States of America 23.0%, Germany 23.0%, Japan 14.0%, South_Korea 11.0%, China 6.0% 2022-12-15 15 35 Alias of B.1.1.529.2.3.20.8.1.2, Germany/USA, S:K147I NA B.1.1.529.2.3.20.8.1.2
CM.8.1.5 Philippines 94.0%, Japan 3.0%, Australia 3.0% 2023-01-10 26 36 Alias of B.1.1.529.2.3.20.8.1.5, S:K150E, S:Y248H, N:A155V, Philippines, from sars-cov-2-variants/lineage-proposals#293 NA B.1.1.529.2.3.20.8.1.5
CM.10 Philippines 41.0%, United States of America 23.0%, Indonesia 10.0%, South_Korea 7.0%, Japan 4.0% 2022-11-01 36 283 Alias of B.1.1.529.2.3.20.10, USA/South Korea/Singapore, S:K478T reversion, S:V445A NA B.1.1.529.2.3.20.10
BA.2.3.21 Philippines 39.0%, United States of America 28.0%, Indonesia 17.0%, Vietnam 11.0%, Thailand 6.0% 2022-02-16 9 18 Alias of B.1.1.529.2.3.21, Philippines, S:P9L and 493 reversion NA B.1.1.529.2.3.21
BA.2.9 Denmark 25.0%, Germany 17.0%, United Kingdom 13.0%, United States of America 10.0%, Sweden 5.0% 2020-07-21 42851 207832 Alias of B.1.1.529.2.9, European lineage, from pango-designation issue #432 NA B.1.1.529.2.9
BA.2.10.1 Australia 24.0%, India 15.0%, United States of America 12.0%, United Kingdom 12.0%, Japan 8.0% 2021-12-23 1668 8605 Alias of B.1.1.529.2.10.1, lineage in Singapore and other countries NA B.1.1.529.2.10.1
BA.2.12.1 United States of America 82.0%, Canada 5.0%, United Kingdom 2.0%, Germany 1.0%, Mexico 1.0% 2020-04-15 39747 275603 Alias of B.1.1.529.2.12.1, USA and Canada lineage, from pango-designation issue #499 NA B.1.1.529.2.12.1
BA.2.13 United States of America 37.0%, Belgium 20.0%, Finland 6.0%, Germany 5.0%, Netherlands 3.0% 2022-01-01 1245 5484 Alias of B.1.1.529.2.13, Europe lineage, from pango-designation issue #531 NA B.1.1.529.2.13
BA.2.23 United Kingdom 76.0%, United States of America 7.0%, Brazil 3.0%, Germany 2.0%, France 2.0% 2020-10-11 6280 16676 Alias of B.1.1.529.2.23, UK lineage, from pango-designation issue #546 NA B.1.1.529.2.23
BA.2.36 Germany 21.0%, France 14.0%, Belgium 14.0%, United Kingdom 13.0%, United States of America 8.0% 2021-11-15 3000 11475 Alias of B.1.1.529.2.36, mainly found in Germany, Belgium, England and Denmark, from pango-designation issue #565 NA B.1.1.529.2.36
BA.2.56 Japan 16.0%, Brazil 14.0%, Spain 10.0%, Germany 9.0%, United States of America 9.0% 2020-06-16 496 6992 Alias of B.1.1.529.2.56, mainly found in Europe, from pango-designation issue #668 NA B.1.1.529.2.56
BA.2.65 United States of America 23.0%, Canada 16.0%, Japan 12.0%, Sweden 9.0%, Germany 9.0% 2021-10-11 2022 7422 Alias of B.1.1.529.2.65, Canada and USA lineage NA B.1.1.529.2.65
BA.2.75 India 67.0%, United States of America 5.0%, Canada 4.0%, Australia 3.0%, Japan 2.0% 2020-08-08 565 4439 Alias of B.1.1.529.2.75, mainly found in India, from pango-designation issue #773 NA B.1.1.529.2.75
BL.1 India 28.0%, United States of America 9.0%, United Kingdom 7.0%, Japan 7.0%, Australia 6.0% 2022-01-03 26 2041 Alias of B.1.1.529.2.75.1.1, mainly found in India from pango-designation issue #944, S:R346T on polytomy NA B.1.1.529.2.75.1.1
BA.2.75.2 India 21.0%, United States of America 17.0%, United Kingdom 9.0%, Australia 8.0%, Canada 5.0% 2022-01-01 1500 5043 Alias of B.1.1.529.2.75.2, mainly found in Asia and Australia, pango-designation issue #963 NA B.1.1.529.2.75.2
BM.1.1.1 India 32.0%, United States of America 12.0%, Singapore 11.0%, Australia 5.0%, South_Korea 4.0% 2022-07-12 224 389 Alias of B.1.1.529.2.75.3.1.1.1, mainly found in India (West Bengal), defined by S:490S From #1043 NA B.1.1.529.2.75.3.1.1.1
CJ.1.1 Singapore 32.0%, Malaysia 18.0%, United Kingdom 14.0%, Japan 11.0%, Canada 6.0% 2022-10-12 11 124 Alias of B.1.1.529.2.75.3.1.1.1.1.1, S:V445A, Singapore/Malaysia/Japan, from issue #1384 NA B.1.1.529.2.75.3.1.1.1.1.1
CJ.1.3 South_Korea 82.0%, Japan 7.0%, Austria 6.0%, Canada 1.0%, Germany 1.0% 2022-11-03 245 1295 Alias of B.1.1.529.2.75.3.1.1.1.1.3, A261G reversion, G4960A, C14790T, South Korea NA B.1.1.529.2.75.3.1.1.1.1.3
CJ.1.3.1 Japan 80.0%, South_Korea 18.0%, China 2.0% 2023-03-17 48 88 Alias of B.1.1.529.2.75.3.1.1.1.1.3.1, S:R214S, ORF1a:G3578S, South Korea/Japan, sars-cov-2-variants/lineage-proposals#287 NA B.1.1.529.2.75.3.1.1.1.1.3.1
CJ.1.3.2 South_Korea 97.0%, Singapore 2.0%, Japan 1.0%, United States of America 1.0% 2022-11-13 198 196 Alias of B.1.1.529.2.75.3.1.1.1.1.3.2, S:D936H, South Korea, sars-cov-2-variants/lineage-proposals#287 NA B.1.1.529.2.75.3.1.1.1.1.3.2
EP.1 Bhutan 39.0%, Canada 15.0%, Singapore 15.0%, Australia 9.0%, Japan 4.0% 2022-12-12 12 46 Alias of B.1.1.529.2.75.3.1.1.4.1, S:L452R, Bhutan, from #1676 NA B.1.1.529.2.75.3.1.1.4.1
EP.2 France 41.0%, Belgium 30.0%, Germany 17.0%, Austria 4.0%, United States of America 4.0% 2022-11-15 33 46 Alias of B.1.1.529.2.75.3.1.1.4.2, S:S1147L, N:G212S, Belgium/Europe NA B.1.1.529.2.75.3.1.1.4.2
BM.4.1.1 United States of America 24.0%, India 22.0%, United Kingdom 11.0%, Australia 6.0%, Singapore 4.0% 2022-07-20 35 917 Alias of B.1.1.529.2.75.3.4.1.1, mainly found in India, defined by S:346T NA B.1.1.529.2.75.3.4.1.1
CH.1.1 United Kingdom 27.0%, Germany 11.0%, United States of America 9.0%, South_Korea 6.0%, Netherlands 4.0% 2022-02-10 4929 19515 Alias of B.1.1.529.2.75.3.4.1.1.1.1, defined by S:L452R, issue #1113 NA B.1.1.529.2.75.3.4.1.1.1.1
CH.1.1.1 United Kingdom 37.0%, Sweden 14.0%, Australia 9.0%, Germany 5.0%, United States of America 5.0% 2022-10-15 2050 6704 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1, defined by S:N185D NA B.1.1.529.2.75.3.4.1.1.1.1.1
DV.1 United Kingdom 56.0%, United States of America 14.0%, Iceland 14.0%, Sweden 3.0%, Canada 2.0% 2022-12-05 187 284 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.1, UK, defined by S:L176F NA B.1.1.529.2.75.3.4.1.1.1.1.1.1
DV.1.1 United Kingdom 42.0%, Canada 28.0%, United States of America 5.0%, Germany 4.0%, Australia 4.0% 2022-11-28 582 1428 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.1.1, defined by S:Q613H and N:T265I, from #1720 NA B.1.1.529.2.75.3.4.1.1.1.1.1.1.1
DV.2 United Kingdom 77.0%, Germany 11.0%, United States of America 3.0%, Austria 3.0%, Canada 1.0% 2022-11-20 71 222 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.2, UK, defined by S:I569V NA B.1.1.529.2.75.3.4.1.1.1.1.1.2
DV.3 United Kingdom 81.0%, Ireland 3.0%, United States of America 3.0%, Greece 2.0%, Germany 1.0% 2022-11-11 256 496 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.3, UK, defined by ORF1a:E377K NA B.1.1.529.2.75.3.4.1.1.1.1.1.3
DV.3.1 Portugal 32.0%, United Kingdom 22.0%, Ireland 8.0%, France 7.0%, Germany 6.0% 2022-11-25 49 167 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.3.1 found mainly in Portugal and UK, from pango-designation issue #1626 NA B.1.1.529.2.75.3.4.1.1.1.1.1.3.1
DV.4 Singapore 38.0%, Japan 23.0%, Malaysia 19.0%, Australia 13.0%, United Kingdom 3.0% 2022-12-01 34 222 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.4, Malaysia/Singapore, S:I714V, from #1617 NA B.1.1.529.2.75.3.4.1.1.1.1.1.4
DV.5 Australia 51.0%, United Kingdom 19.0%, Finland 17.0%, New_Zealand 4.0%, Italy 2.0% 2023-01-06 38 191 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.5, England/Australia, ORF1a:R24C, S:613H, from #1753 NA B.1.1.529.2.75.3.4.1.1.1.1.1.5
DV.6 United Kingdom 64.0%, Germany 6.0%, Denmark 3.0%, Spain 3.0%, Finland 3.0% 2022-11-13 1384 3544 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6, T15591C NA B.1.1.529.2.75.3.4.1.1.1.1.1.6
DV.6.1 Finland 25.0%, Poland 17.0%, Germany 16.0%, Denmark 8.0%, Austria 8.0% 2023-01-20 116 146 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.1, S:Q613H, T15591C, Central Europe NA B.1.1.529.2.75.3.4.1.1.1.1.1.6.1
DV.6.2 Japan 26.0%, South_Korea 20.0%, United States of America 10.0%, Austria 10.0%, Singapore 5.0% 2023-02-13 145 315 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.2, S:Q613H, C6628T, Asia From #2045 NA B.1.1.529.2.75.3.4.1.1.1.1.1.6.2
DV.7 United Kingdom 69.0%, Germany 8.0%, Canada 6.0%, United States of America 5.0%, Sweden 2.0% 2023-01-19 226 264 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7, S:L858I, ORF1a:A3548V, England, from #2038 NA B.1.1.529.2.75.3.4.1.1.1.1.1.7
DV.7.1 Spain 57.0%, Ireland 11.0%, United States of America 11.0%, United Kingdom 7.0%, Israel 6.0% 2023-05-11 73 205 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1, S:L455F, S:F456L, Spain/Austria, from sars-cov-2-variants/lineage-proposals#135 NA B.1.1.529.2.75.3.4.1.1.1.1.1.7.1
DV.7.2 United Kingdom 91.0%, United States of America 3.0%, Canada 3.0%, France 3.0% 2023-03-14 33 33 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.2, C703T, England NA B.1.1.529.2.75.3.4.1.1.1.1.1.7.2
DV.8 Sweden 80.0%, Finland 5.0%, Norway 4.0%, Denmark 2.0%, United States of America 2.0% 2023-01-07 164 197 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.8, S:Q613H, C8299T, C19602T, Sweden NA B.1.1.529.2.75.3.4.1.1.1.1.1.8
CH.1.1.2 United Kingdom 42.0%, United States of America 10.0%, Germany 9.0%, Denmark 7.0%, Canada 6.0% 2022-10-23 19 2264 Alias of B.1.1.529.2.75.3.4.1.1.1.1.2, defined by S:T883I, ORF1a:Y1846C, ORF1a:G2294S on T27576C branch NA B.1.1.529.2.75.3.4.1.1.1.1.2
CH.1.1.3 New_Zealand 49.0%, Australia 19.0%, United Kingdom 7.0%, Germany 6.0%, Hong_Kong 4.0% 2022-10-18 99 766 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3, S:S255P, New Zealand/Australia/Hong Kong, from #1405 NA B.1.1.529.2.75.3.4.1.1.1.1.3
GQ.1 Australia 59.0%, New_Zealand 26.0%, United States of America 4.0%, United Kingdom 4.0%, Canada 1.0% 2023-02-24 32 68 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1, S:486P, ORF1a:H1545Q, ORF1b:V1520L, Australia/New Zealand, from #1872 NA B.1.1.529.2.75.3.4.1.1.1.1.3.1
GQ.1.1 New_Zealand 98.0%, Australia 2.0% 2023-04-21 20 40 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1.1, S:G213E, New Zealand, from sars-cov-2-variants/lineage-proposals#343 NA B.1.1.529.2.75.3.4.1.1.1.1.3.1.1
CH.1.1.5 Denmark 61.0%, United Kingdom 26.0%, United States of America 4.0%, Sweden 4.0%, Slovenia 2.0% 2022-11-09 82 391 Alias of B.1.1.529.2.75.3.4.1.1.1.1.5, ORF3a:P104S, found mainly in Denmark and UK, from pango-designation issue #1539 NA B.1.1.529.2.75.3.4.1.1.1.1.5
CH.1.1.6 United Kingdom 91.0%, Ireland 2.0%, United States of America 1.0%, Luxembourg 1.0%, Spain 1.0% 2022-11-15 122 495 Alias of B.1.1.529.2.75.3.4.1.1.1.1.6, UK, defined by S:T732I NA B.1.1.529.2.75.3.4.1.1.1.1.6
CH.1.1.7 New_Zealand 52.0%, Australia 34.0%, United States of America 4.0%, Japan 4.0%, United Kingdom 1.0% 2022-10-05 618 1325 Alias of B.1.1.529.2.75.3.4.1.1.1.1.7, New Zealand/Australia, defined by ORF1a:F143C NA B.1.1.529.2.75.3.4.1.1.1.1.7
CH.1.1.8 United Kingdom 52.0%, Ireland 38.0%, Germany 3.0%, Denmark 2.0%, Switzerland 2.0% 2022-11-05 99 329 Alias of B.1.1.529.2.75.3.4.1.1.1.1.8, Ireland, defined by S:A846V NA B.1.1.529.2.75.3.4.1.1.1.1.8
CH.1.1.9 United Kingdom 92.0%, Germany 2.0%, United States of America 1.0%, Sweden 1.0%, Denmark 1.0% 2022-11-15 128 214 Alias of B.1.1.529.2.75.3.4.1.1.1.1.9, England, defined by S:I1232V NA B.1.1.529.2.75.3.4.1.1.1.1.9
CH.1.1.10 Ireland 41.0%, United Kingdom 38.0%, Netherlands 6.0%, Denmark 2.0%, Germany 2.0% 2022-10-23 548 821 Alias of B.1.1.529.2.75.3.4.1.1.1.1.10, Ireland, ORF1a:G442S NA B.1.1.529.2.75.3.4.1.1.1.1.10
CH.1.1.11 United Kingdom 12.0%, Australia 12.0%, Germany 11.0%, Japan 7.0%, Hong_Kong 7.0% 2022-03-03 709 1548 Alias of B.1.1.529.2.75.3.4.1.1.1.1.11, ORF1a:A1176T NA B.1.1.529.2.75.3.4.1.1.1.1.11
GP.1 Italy 31.0%, United Kingdom 20.0%, Ireland 9.0%, Australia 9.0%, Netherlands 6.0% 2022-11-27 119 185 Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.1, S:Q52H, ORF7a:T28I, Europe NA B.1.1.529.2.75.3.4.1.1.1.1.11.1
GP.2 Germany 35.0%, United Kingdom 14.0%, Denmark 8.0%, Sweden 5.0%, Austria 5.0% 2022-08-01 780 788 Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.2, ORF6:S41F, T13450C, Europe NA B.1.1.529.2.75.3.4.1.1.1.1.11.2
GP.3 Ireland 45.0%, United Kingdom 19.0%, France 6.0%, Germany 6.0%, Netherlands 5.0% 2022-11-07 392 376 Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.3, T5218C, A16878G, A26519G, C29236T, Ireland NA B.1.1.529.2.75.3.4.1.1.1.1.11.3
CH.1.1.12 Denmark 84.0%, Austria 3.0%, Germany 3.0%, Sweden 3.0%, Netherlands 2.0% 2022-11-25 202 618 Alias of B.1.1.529.2.75.3.4.1.1.1.1.12, S:L858I on ORF1a:A486V branch, Denmark NA B.1.1.529.2.75.3.4.1.1.1.1.12
FS.1 Denmark 77.0%, Portugal 6.0%, France 4.0%, United Kingdom 3.0%, Sweden 2.0% 2022-12-30 135 270 Alias of B.1.1.529.2.75.3.4.1.1.1.1.12.1, found mainly in Denmark, from pango-designation issue #1816 NA B.1.1.529.2.75.3.4.1.1.1.1.12.1
CH.1.1.13 United Kingdom 91.0%, Denmark 3.0%, United States of America 1.0%, Norway 1.0%, Netherlands 1.0% 2022-12-02 227 267 Alias of B.1.1.529.2.75.3.4.1.1.1.1.13, ORF3a:S171L NA B.1.1.529.2.75.3.4.1.1.1.1.13
CH.1.1.14 United Kingdom 61.0%, Canada 7.0%, Belgium 6.0%, Germany 4.0%, United States of America 4.0% 2022-10-19 125 267 Alias of B.1.1.529.2.75.3.4.1.1.1.1.14, N:T362I NA B.1.1.529.2.75.3.4.1.1.1.1.14
CH.1.1.15 Lithuania 31.0%, Germany 24.0%, United Kingdom 19.0%, Denmark 4.0%, Norway 3.0% 2022-11-24 159 557 Alias of B.1.1.529.2.75.3.4.1.1.1.1.15, found mainly in Lithuania, Germany and UK, from pango-designation issue #1726 NA B.1.1.529.2.75.3.4.1.1.1.1.15
CH.1.1.16 Germany 31.0%, Sweden 30.0%, Denmark 7.0%, Austria 5.0%, United Kingdom 4.0% 2022-12-07 83 322 Alias of B.1.1.529.2.75.3.4.1.1.1.1.16, S:613H, ORF3a:S26L, on C193T branch, Germany/Sweden, from #1753 NA B.1.1.529.2.75.3.4.1.1.1.1.16
CH.1.1.17 Australia 45.0%, New_Zealand 23.0%, Solomon_Islands 14.0%, United Kingdom 9.0%, Papua_New_Guinea 6.0% 2022-10-13 125 244 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17, M:S212G, on C21811T branch, from #1753 NA B.1.1.529.2.75.3.4.1.1.1.1.17
FK.1 New_Zealand 60.0%, Australia 22.0%, South_Korea 6.0%, United States of America 6.0%, Austria 1.0% 2023-01-28 23 413 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1, found mainly in New Zealand and Australia, from pango-designation issue #1718 NA B.1.1.529.2.75.3.4.1.1.1.1.17.1
FK.1.1 New_Zealand 32.0%, Australia 29.0%, South_Korea 14.0%, United States of America 11.0%, Japan 6.0% 2023-02-08 53 1210 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1, ORF1a:A1060T, on C27804T>ORF1b:L2580I>N:G34E branch, New Zealand, from #1881 NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.1
FK.1.1.1 Australia 97.0%, New_Zealand 3.0% 2023-04-23 21 33 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.1, S:V445A, Australia From sars-cov-2-variants/lineage-proposals#368 NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.1
FK.1.1.2 Australia 51.0%, New_Zealand 39.0%, Japan 3.0%, United States of America 3.0%, Canada 1.0% 2023-03-04 726 757 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.2, C9223T, T23071G NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.2
FK.1.2 Slovenia 30.0%, New_Zealand 28.0%, Austria 20.0%, United Kingdom 10.0%, Denmark 3.0% 2023-01-22 98 115 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2, ORF1a:L384F, ORF1a:R550H NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.2
FK.1.2.1 Finland 32.0%, Denmark 28.0%, Germany 12.0%, Netherlands 8.0%, Austria 6.0% 2023-02-04 174 251 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.1, ORF1a:T891I, Germany/Denmark/Finland/Austria NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.1
FK.1.2.2 New_Zealand 38.0%, Australia 22.0%, United States of America 19.0%, South_Korea 7.0%, Canada 6.0% 2023-02-15 113 137 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.2, ORF1a:D139N, ORF1a:R226K, ORF1a:Q556K, ORF3a:T64N, T11737C, AUS/NZ NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.2
FK.1.3 Australia 75.0%, United States of America 22.0%, Sweden 1.0%, Japan 1.0% 2023-02-18 24 67 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3, ORF1b:M1839I, on C27804T>ORF1b:L2580I>N:G34E branch, Australia NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.3
FK.1.3.1 Australia 96.0%, United States of America 4.0% 2023-02-20 54 57 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.1, S:E583D, Australia NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.1
FK.1.3.2 Japan 60.0%, Australia 32.0%, United States of America 3.0%, South_Korea 2.0%, Finland 1.0% 2023-03-09 181 352 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.2, C9391T, T13596C, Australia/Japan NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.2
FK.1.4 Australia 100.0% 2023-02-01 49 130 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.4, S:S704L, on C27804>ORF7a:Y40H branch, Australia NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.4
FK.1.4.1 Australia 81.0%, Puerto_Rico 12.0%, United States of America 6.0% 2023-04-01 34 32 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.4.1, S:G181A, Australia/Puerto Rico From sars-cov-2-variants/lineage-proposals#88 NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.4.1
FK.1.5 Australia 53.0%, New_Zealand 15.0%, United States of America 14.0%, Canada 10.0%, Sweden 4.0% 2023-02-20 205 227 Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.5, G5155A, C12439T, Australia/New Zealand NA B.1.1.529.2.75.3.4.1.1.1.1.17.1.5
CH.1.1.18 United Kingdom 28.0%, United States of America 23.0%, Germany 17.0%, Austria 6.0%, India 5.0% 2022-10-03 173 248 Alias of B.1.1.529.2.75.3.4.1.1.1.1.18, S:K187T, related to #1747 NA B.1.1.529.2.75.3.4.1.1.1.1.18

Creating a PangoRo object

Most of the functions refer to a designated object (S3) in R. This allows one to specify how one wants to operate with the alias conversions. For instance, the object can be created to be in an ‘offline’ mode.

my_pangoro <- pangoro()

my_pangoro
    alias                            lineage
1       A                                   
2       B                                   
3       C                            B.1.1.1
4       D                           B.1.1.25
5       G                          B.1.258.2
6       K                          B.1.1.277
7       L                           B.1.1.10
8       M                          B.1.1.294
9       N                           B.1.1.33
10      P                           B.1.1.28
11      Q                            B.1.1.7
12      R                          B.1.1.316
13      S                          B.1.1.217
14      U                         B.1.177.60
15      V                         B.1.177.54
16      W                         B.1.177.53
17      Y                         B.1.177.52
18      Z                         B.1.177.50
19     AA                         B.1.177.15
20     AB                         B.1.160.16
21     AC                          B.1.1.405
22     AD                          B.1.1.315
23     AE                          B.1.1.306
24     AF                          B.1.1.305
25     AG                          B.1.1.297
26     AH                          B.1.1.241
27     AJ                          B.1.1.240
28     AK                          B.1.1.232
29     AL                          B.1.1.231
30     AM                          B.1.1.216
31     AN                          B.1.1.200
32     AP                           B.1.1.70
33     AQ                           B.1.1.39
34     AS                          B.1.1.317
35     AT                          B.1.1.370
36     AU                          B.1.466.2
37     AV                          B.1.1.482
38     AW                          B.1.1.464
39     AY                          B.1.617.2
40     AZ                          B.1.1.318
41     BA                          B.1.1.529
42     BB                          B.1.621.1
43     BC                    B.1.1.529.1.1.1
44     BD                   B.1.1.529.1.17.2
45     BE                    B.1.1.529.5.3.1
46     BF                    B.1.1.529.5.2.1
47     BG                   B.1.1.529.2.12.1
48     BH                   B.1.1.529.2.38.3
49     BJ                   B.1.1.529.2.10.1
50     BK                   B.1.1.529.5.1.10
51     BL                   B.1.1.529.2.75.1
52     BM                   B.1.1.529.2.75.3
53     BN                   B.1.1.529.2.75.5
54     BP                   B.1.1.529.2.3.16
55     BQ              B.1.1.529.5.3.1.1.1.1
56     BR                   B.1.1.529.2.75.4
57     BS                    B.1.1.529.2.3.2
58     BT                   B.1.1.529.5.1.21
59     BU                   B.1.1.529.5.2.16
60     BV                   B.1.1.529.5.2.20
61     BW                    B.1.1.529.5.6.2
62     BY                   B.1.1.529.2.75.6
63     BZ                    B.1.1.529.5.2.3
64     CA                   B.1.1.529.2.75.2
65     CB                   B.1.1.529.2.75.9
66     CC              B.1.1.529.5.3.1.1.1.2
67     CD                   B.1.1.529.5.2.31
68     CE                   B.1.1.529.5.2.33
69     CF                   B.1.1.529.5.2.27
70     CG                   B.1.1.529.5.2.26
71     CH             B.1.1.529.2.75.3.4.1.1
72     CJ             B.1.1.529.2.75.3.1.1.1
73     CK                   B.1.1.529.5.2.24
74     CL                   B.1.1.529.5.1.29
75     CM                   B.1.1.529.2.3.20
76     CN                   B.1.1.529.5.2.21
77     CP                    B.1.1.529.5.2.6
78     CQ              B.1.1.529.5.3.1.4.1.1
79     CR                   B.1.1.529.5.2.18
80     CS                   B.1.1.529.4.1.10
81     CT                   B.1.1.529.5.2.36
82     CU                   B.1.1.529.5.1.26
83     CV             B.1.1.529.2.75.3.1.1.3
84     CW       B.1.1.529.5.3.1.1.1.1.1.1.14
85     CY                    B.1.1.529.5.2.7
86     CZ        B.1.1.529.5.3.1.1.1.1.1.1.1
87     DA                   B.1.1.529.5.2.38
88     DB                   B.1.1.529.5.2.25
89     DC                    B.1.1.529.4.6.5
90     DD                   B.1.1.529.2.3.21
91     DE                   B.1.1.529.5.1.23
92     DF                   B.1.1.529.5.10.1
93     DG             B.1.1.529.5.2.24.2.1.1
94     DH                   B.1.1.529.5.1.22
95     DJ                   B.1.1.529.5.1.25
96     DK        B.1.1.529.5.3.1.1.1.1.1.1.7
97     DL                   B.1.1.529.5.1.15
98     DM       B.1.1.529.5.3.1.1.1.1.1.1.15
99     DN        B.1.1.529.5.3.1.1.1.1.1.1.5
100    DP        B.1.1.529.5.3.1.1.1.1.1.1.8
101    DQ                   B.1.1.529.5.2.47
102    DR        B.1.1.529.5.3.1.1.1.1.1.1.3
103    DS             B.1.1.529.2.75.5.1.3.1
104    DT       B.1.1.529.5.3.1.1.1.1.1.1.32
105    DU        B.1.1.529.5.3.1.1.1.1.1.1.2
106    DV       B.1.1.529.2.75.3.4.1.1.1.1.1
107    DW              B.1.1.529.5.3.1.1.2.1
108    DY                   B.1.1.529.5.2.48
109    DZ                   B.1.1.529.5.2.49
110    EA       B.1.1.529.5.3.1.1.1.1.1.1.52
111    EB                   B.1.1.529.5.1.35
112    EC       B.1.1.529.5.3.1.1.1.1.1.10.1
113    ED       B.1.1.529.5.3.1.1.1.1.1.1.18
114    EE        B.1.1.529.5.3.1.1.1.1.1.1.4
115    EF       B.1.1.529.5.3.1.1.1.1.1.1.13
116    EG                          XBB.1.9.2
117    EH       B.1.1.529.5.3.1.1.1.1.1.1.28
118    EJ             B.1.1.529.2.75.5.1.3.8
119    EK                         XBB.1.5.13
120    EL                         XBB.1.5.14
121    EM                          XBB.1.5.7
122    EN       B.1.1.529.5.3.1.1.1.1.1.1.46
123    EP             B.1.1.529.2.75.3.1.1.4
124    EQ                   B.1.1.529.5.1.33
125    ER       B.1.1.529.5.3.1.1.1.1.1.1.22
126    ES       B.1.1.529.5.3.1.1.1.1.1.1.65
127    ET       B.1.1.529.5.3.1.1.1.1.1.1.35
128    EU                         XBB.1.5.26
129    EV       B.1.1.529.5.3.1.1.1.1.1.1.71
130    EW       B.1.1.529.5.3.1.1.1.1.1.1.38
131    EY B.1.1.529.5.3.1.1.1.1.1.1.13.1.1.1
132    EZ       B.1.1.529.5.3.1.1.1.1.1.1.43
133    FA       B.1.1.529.5.3.1.1.1.1.1.1.10
134    FB        B.1.1.529.5.3.1.1.1.1.1.2.1
135    FC       B.1.1.529.5.3.1.1.1.1.1.1.72
136    FD                         XBB.1.5.15
137    FE                         XBB.1.18.1
138    FF        B.1.1.529.5.3.1.1.1.1.1.8.2
139    FG                         XBB.1.5.16
140    FH                         XBB.1.5.17
141    FJ      B.1.1.529.2.75.3.4.1.1.1.1.19
142    FK      B.1.1.529.2.75.3.4.1.1.1.1.17
143    FL                          XBB.1.9.1
144    FM       B.1.1.529.5.3.1.1.1.1.1.1.53
145    FN       B.1.1.529.5.3.1.1.1.1.1.1.74
146    FP                         XBB.1.11.1
147    FQ       B.1.1.529.5.3.1.1.1.1.1.1.39
148    FR             B.1.1.529.2.75.5.1.2.3
149    FS      B.1.1.529.2.75.3.4.1.1.1.1.12
150    FT                         XBB.1.5.39
151    FU                         XBB.1.16.1
152    FV             B.1.1.529.2.3.20.8.1.1
153    FW                         XBB.1.28.1
154    FY                         XBB.1.22.1
155    FZ                         XBB.1.5.47
156    GA                         XBB.1.17.1
157    GB                         XBB.1.5.46
158    GC                         XBB.1.5.21
159    GD                          XBB.1.9.3
160    GE                         XBB.2.3.10
161    GF                         XBB.1.5.24
162    GG                         XBB.1.5.38
163    GH                          XBB.2.6.1
164    GJ                          XBB.2.3.3
165    GK                         XBB.1.5.70
166    GL                          XAY.1.1.1
167    GM                          XBB.2.3.6
168    GN                         XBB.1.5.73
169    GP      B.1.1.529.2.75.3.4.1.1.1.1.11
170    GQ       B.1.1.529.2.75.3.4.1.1.1.1.3
171    GR                         XBB.1.5.42
172    GS                         XBB.2.3.11
173    GT                          XBC.1.6.1
174    GU                         XBB.1.5.41
175    GV                         XBB.1.5.48
176    GW                         XBB.1.19.1
177    GY                         XBB.1.16.2
178    GZ                          XBB.2.3.4
179    HA                         XBB.1.5.86
180    HB                         XBB.1.34.2
181    HC                         XBB.1.5.44
182    HD                         XBB.1.5.93
183    HE                   XBB.1.18.1.1.1.1
184    HF                        XBB.1.16.13
185    HG                          XBB.2.3.8
186    HH                          XBB.2.3.2
187    HJ                          XBB.1.5.1
188    HK                    XBB.1.9.2.5.1.1
189    HL                         XBB.1.42.2
190    HM                         XBB.1.5.30
191    HN                    XBB.1.9.1.1.5.1
192    HP                         XBB.1.5.55
193    HQ                         XBB.1.5.92
194    HR                         XBB.1.5.77
195    HS                         XBB.1.5.95
196    HT                         XBB.1.5.49
197    HU                         XBB.1.22.2
198    HV                    XBB.1.9.2.5.1.6
199    HW                          XBC.1.6.3
200    HY                        XBB.1.5.100
201    HZ                         XBB.1.5.68
202    JA                         XBB.2.3.13
203    JB                         XBB.1.5.53
204    JC                         XBB.1.41.1
205    JD                        XBB.1.5.102
206    JE                    XBB.2.3.3.1.2.1
207    JF                         XBB.1.16.6
208    XA                            B.1.1.7
209    XA                            B.1.177
210    XB                            B.1.634
211    XB                            B.1.631
212    XC                              AY.29
213    XC                            B.1.1.7
214    XD                          B.1.617.2
215    XD                               BA.1
216    XE                               BA.1
217    XE                               BA.2
218    XF                          B.1.617.2
219    XF                               BA.1
220    XG                               BA.1
221    XG                               BA.2
222    XH                               BA.1
223    XH                               BA.2
224    XJ                               BA.1
225    XJ                               BA.2
226    XK                               BA.1
227    XK                               BA.2
228    XL                               BA.1
229    XL                               BA.2
230    XM                             BA.1.1
231    XM                               BA.2
232    XN                               BA.1
233    XN                               BA.2
234    XP                             BA.1.1
235    XP                               BA.2
236    XQ                             BA.1.1
237    XQ                               BA.2
238    XR                             BA.1.1
239    XR                               BA.2
240    XS                          B.1.617.2
241    XS                             BA.1.1
242    XT                               BA.2
243    XT                               BA.1
244    XU                               BA.1
245    XU                               BA.2
246    XV                               BA.1
247    XV                               BA.2
248    XW                               BA.1
249    XW                               BA.2
250    XY                               BA.1
251    XY                               BA.2
252    XZ                               BA.2
253    XZ                               BA.1
254   XAA                               BA.1
255   XAA                               BA.2
256   XAB                               BA.1
257   XAB                               BA.2
258   XAC                               BA.2
259   XAC                               BA.1
260   XAC                               BA.2
261   XAD                               BA.2
262   XAD                               BA.1
263   XAE                               BA.2
264   XAE                               BA.1
265   XAF                               BA.1
266   XAF                               BA.2
267   XAG                               BA.1
268   XAG                               BA.2
269   XAH                               BA.2
270   XAH                               BA.1
271   XAJ                          BA.2.12.1
272   XAJ                               BA.4
273   XAK                               BA.2
274   XAK                               BA.1
275   XAK                               BA.2
276   XAL                               BA.1
277   XAL                               BA.2
278   XAM                             BA.1.1
279   XAM                             BA.2.9
280   XAN                               BA.2
281   XAN                             BA.5.1
282   XAP                               BA.2
283   XAP                               BA.1
284   XAQ                               BA.1
285   XAQ                               BA.2
286   XAR                               BA.1
287   XAR                               BA.2
288   XAS                               BA.5
289   XAS                               BA.2
290   XAT                          BA.2.3.13
291   XAT                               BA.1
292   XAU                             BA.1.1
293   XAU                             BA.2.9
294   XAV                               BA.2
295   XAV                               BA.5
296   XAW                               BA.2
297   XAW                             AY.122
298   XAY                               BA.2
299   XAY                              AY.45
300   XAY                               BA.2
301   XAY                              AY.45
302   XAY                               BA.2
303   XAZ                             BA.2.5
304   XAZ                               BA.5
305   XAZ                             BA.2.5
306   XBA                               BA.2
307   XBA                              AY.45
308   XBA                               BA.2
309   XBA                              AY.45
310   XBA                               BA.2
311   XBB                               BJ.1
312   XBB                           BM.1.1.1
313   XBC                               BA.2
314   XBC                          B.1.617.2
315   XBC                               BA.2
316   XBC                          B.1.617.2
317   XBD                          BA.2.75.2
318   XBD                               BF.5
319   XBE                             BA.5.2
320   XBE                             BE.4.1
321   XBF                           BA.5.2.3
322   XBF                               CJ.1
323   XBG                            BA.2.76
324   XBG                             BA.5.2
325   XBH                          BA.2.3.17
326   XBH                          BA.2.75.2
327   XBJ                          BA.2.3.20
328   XBJ                             BA.5.2
329   XBK                             BA.5.2
330   XBK                               CJ.1
331   XBL                         XBB.1.5.57
332   XBL                            BA.2.75
333   XBL                         XBB.1.5.57
334   XBM                            BA.2.76
335   XBM                               BF.3
336   XBN                            BA.2.75
337   XBN                              XBB.3
338   XBP                            BA.2.75
339   XBP                               BQ.1
340   XBQ                             BA.5.2
341   XBQ                               CJ.1
342   XBR                            BA.2.75
343   XBR                               BQ.1
344   XBS                            BA.2.75
345   XBS                               BQ.1
346   XBT                          BA.5.2.34
347   XBT                            BA.2.75
348   XBT                          BA.5.2.34
349   XBU                          BA.2.75.3
350   XBU                               BQ.1
351   XBU                          BA.2.75.3
352   XBV                               CR.1
353   XBV                              XBB.1
354   XBW                            XBB.1.5
355   XBW                            BQ.1.14
356   XBY                             BR.2.1
357   XBY                                XBF
358   XBZ                             BA.5.2
359   XBZ                             EF.1.3
360   XCA                            BA.2.75
361   XCA                               BQ.1
362   XCB                            BF.31.1
363   XCB                            BQ.1.10
364   XCC                           CH.1.1.1
365   XCC                          XBB.1.9.1
366   XCD                              XBB.1
367   XCD                          BQ.1.1.25
368   XCE                               BQ.1
369   XCE                               FY.1
370   XCF                                XBB
371   XCF                               FE.1
372   XCG                             BA.5.2
373   XCG                              XBB.1
374   XCH                             GK.1.3
375   XCH                            XBB.1.9
376   XCH                             GK.1.3
377   XCJ                               GM.2
378   XCJ                               FP.1
379   XCJ                               GM.2

Basic Commands: Expand & Collapse

my_pangoro |> 
  expand_pangoro(c('BA.1', 'BM.1')) |>
  data.frame(fix.empty.names = FALSE)
                       
BA.1        B.1.1.529.1
BM.1 B.1.1.529.2.75.3.1


my_pangoro |> 
  collapse_pangoro(c('B.1.1.529.1', 'B.1.1.529.2.75.3.1'))
[1] "BA.1" "BM.1"

Basic Commands: Sort

Take lineage list and place in semi-sorted order.

# Perform linear sort
sorted_lin <- sort_pangoro(my_pangoro,
                           c('BL.1', 'BA.1', 'BM.1', 'BQ.3'))

# Examine sort after expanded from aliases
expand_pangoro(my_pangoro, sorted_lin) |>
  data.frame(fix.empty.names = FALSE)
                            
BA.1             B.1.1.529.1
BL.1      B.1.1.529.2.75.1.1
BM.1      B.1.1.529.2.75.3.1
BQ.3 B.1.1.529.5.3.1.1.1.1.3

Advanced Use: Programmatic Look Ups

Group lineage list into:

  1. BA.2
  2. Recombinant
  3. Other

Dummy Data-set


Tally of COVID-19 Lineages as Aliases
COVID-19 Lineages N
AY 1
B.1.1.529.1.1 14
B.1.1.529.2 5
B.1.617.2 2
BE 15
BL 13
BQ 7
CC 11
EF 8
XAY 6
XBB 9

Advanced Use Continued…

Examine lineages and expand aliases from covid_lineages data set.

exp_lin <- my_pangoro |>
  expand_pangoro(unique(covid_lineages))

exp_lin
                     B.1.617.2                    B.1.1.529.2 
                   "B.1.617.2"                  "B.1.1.529.2" 
                            BE                             BL 
             "B.1.1.529.5.3.1"             "B.1.1.529.2.75.1" 
                            BQ                             CC 
       "B.1.1.529.5.3.1.1.1.1"        "B.1.1.529.5.3.1.1.1.2" 
                            AY                             EF 
                   "B.1.617.2" "B.1.1.529.5.3.1.1.1.1.1.1.13" 
                           XBB                            XAY 
                         "XBB"                          "XAY" 
                 B.1.1.529.1.1 
               "B.1.1.529.1.1" 

Advanced Use Continued…

Create look-up based on index matching in searches.

# Create index for groups
index_match_ba2 <- mapply('BA.2', unique(covid_lineages),
                          FUN = \(x, y) search_pangoro(my_pangoro, x, y),
                          USE.NAMES = FALSE)
index_match_recom <- startsWith(exp_lin, 'X')

# Create initial data set
lineage_lu <- data.frame(Grouping = 'Other',
                         Source = unique(covid_lineages),
                         Expanded = exp_lin, row.names = NULL)

# Overwite using index with groupings
lineage_lu[index_match_ba2, 'Grouping'] <- 'BA.2'
lineage_lu[index_match_recom, 'Grouping'] <- 'Recombinant'

lineage_lu |>
  knitr::kable(table.attr = "style=\"width: 100%\"") |>
  kableExtra::scroll_box() |> 
  kableExtra::kable_styling(font_size = 20,
                            bootstrap_options = 'striped', 
                            fixed_thead = list(enabled = TRUE,
                                               background = 'black'))

Advanced Use Continued…

Grouping Source Expanded
Other B.1.617.2 B.1.617.2
BA.2 B.1.1.529.2 B.1.1.529.2
Other BE B.1.1.529.5.3.1
BA.2 BL B.1.1.529.2.75.1
Other BQ B.1.1.529.5.3.1.1.1.1
Other CC B.1.1.529.5.3.1.1.1.2
Other AY B.1.617.2
Other EF B.1.1.529.5.3.1.1.1.1.1.1.13
Recombinant XBB XBB
Recombinant XAY XAY
Other B.1.1.529.1.1 B.1.1.529.1.1

Advanced Use Continued…

Merge back to original data set.

merge(data.frame(lineage = covid_lineages),
      lineage_lu,
      by.x = 'lineage', by.y = 'Source') |>
  knitr::kable(table.attr = "style=\"width: 100%\"") |> 
  kableExtra::scroll_box(height = '300px') |> 
  kableExtra::kable_styling(font_size = 20,
                            bootstrap_options = 'striped', 
                            fixed_thead = list(enabled = TRUE,
                                               background = 'black'))
lineage Grouping Expanded
AY Other B.1.617.2
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.1.1 Other B.1.1.529.1.1
B.1.1.529.2 BA.2 B.1.1.529.2
B.1.1.529.2 BA.2 B.1.1.529.2
B.1.1.529.2 BA.2 B.1.1.529.2
B.1.1.529.2 BA.2 B.1.1.529.2
B.1.1.529.2 BA.2 B.1.1.529.2
B.1.617.2 Other B.1.617.2
B.1.617.2 Other B.1.617.2
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BE Other B.1.1.529.5.3.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BL BA.2 B.1.1.529.2.75.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
BQ Other B.1.1.529.5.3.1.1.1.1
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
CC Other B.1.1.529.5.3.1.1.1.2
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
EF Other B.1.1.529.5.3.1.1.1.1.1.1.13
XAY Recombinant XAY
XAY Recombinant XAY
XAY Recombinant XAY
XAY Recombinant XAY
XAY Recombinant XAY
XAY Recombinant XAY
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB
XBB Recombinant XBB

Questions?

{pangoRo}